Jace,
FYI, the trumpet in "The Great Pagoda of Funn" is using a Harmon Mute. Miles Davis used the Harmon Mute a lot in his work.
As an expanded response to Sheep and the "Obscure Notes", you need to have a decent grasp on jazz music and theory to really hear what's going on in the song (along with most of the Fagen/Dan stuff). The notes are not random, there are very much within the realm of correct tones. Perhaps you're feeling your ear bent by the use of leading tones as the chord changes progress.
A final note on "The Great Pagoda of Funn", I think the guitar solo at the end of the song gets too little credit. While I was wowed by the trumpet solo on my first few listens, I find myself liking the guitar solo more and more. It has a very understated rhythm and style (no, not pace
). I really like the melody lines the player is choosing, as well as the phrasing. I think if you give it some time, you'll enjoy the groovetastic nature that it presents.